Step by step tutorial 8 working with shapes

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Step by step tutorial: Working with shapes in ModestR

http://www.ipez.es/ModestR/

What do you need for this tutorial:

1. ModestR v4.0 or higher

2. Environmental data already integrated in ModestR (if you have not done that yet, tutorial “How to

integrate and use environmental data in ModestR” can help you doing that; available in ModestR web site)

3. ModestR database with distribution maps4. About 45 minutes*

ModestR software can be freely downloaded from http://www.ipez.es/ModestR


*Processing times can vary depending on the size of ModestR database and number of environmental variables

http://www.ipez.es/ModestR/Manual_Tutorial.html

http://www.ipez.es/ModestR



We’ll describe how to work with vector layers based on georeferenced shapes in ModestR, introducing some features using global geospatial data of river

basins. Follow the next steps!



The first step is to run MRFinder and go to menu File/Open Database to open your ModestR database containing taxonomical information and distribution maps of several species*


Go to menu File/Open Database and select your database (.ModestRDB)*

*If you don’t have a ModestR database yet, follow the tutorial “How to create a ModestR database” (available in ModestR web site) to create a new one.

In this example, we used a database with 69 species of family Alestidae


http://www.ipez.es/ModestR/Manual_Tutorial.html

ModestR integrates two global geographic databases (ModestR shapes) based on vector layers composed of georeferencedshapes: World Basins and World Countries (administrative divisions). Users could also add their own databases.


1. Go to menu Layers/Add predefined shapes

2. Click on World Basins

In this tutorial, we use geospatial data of global river basins


Shapes are hierarchically organized, from upper levels (e.g., main river basins) to lower levels (e.g., small sub-basins).


BROWSER (HIERARCHICAL TREE) ACTIVE PREVIEW

The user can movethrough the levelsusing the browser(tree) or the activepreview, by double-clicking on thewanted polygon togo into thecorresponding sub-level

Double- Click on theAfrican continent


Now, basins of the African continent are shown. User can go to another sub-level or select any of the displayed basins to be added to the map and processed in later steps.



When the user select a river basin, the tree and the active preview are always synchronized, so that it is easy to know the name of the basin as well as its location in the map. In this example, we select three basins.


To select an element in the active preview,

right click in the desired element and

click on Select element on the pop

up menu.

Click on Close button to add the selected basins to the map


The selected basins are shown and zoomed in the World map. In MRFinder, shapes define an area to search for species


Click on Search button to search for species in

the selected basins


MFFinder provide different search options using a tabbed panel. In this example, we run the search using default options.


Click on Search button to continue

Habitat: User can select the habitats in the selected areas where species will be searched.

Species: User can delimit the rank or species to be searched. If the filter is empty, all the species included in

the database are searched.

Grouping and simplify: Users can choose to search in each region separately or in all regions as a whole. There is an

also an option to simplify the search with complex selections


When the species search in completed, MRFinder shows the Filter/Export tabbed panel. Results are organized in a hierarchical tree with the complete taxonomy.


Search results are shown using a

hierarchical tree with the complete taxonomy


The Filter/Export tabbed panel provide three options to filter the search results: Taxonomy filter, Rare species filter and Categories filter. Final results are shown in tab Filtered results organized in a hierarchical tree with taxonomic information. In this example, we did not apply any filter.


Filtered results are shown using a

hierarchical tree with the complete taxonomy.

User can manually check if any species or taxon is present in the

filtered results

Tabs with different filter options. More details in ModestR manual (Section 3.8)


The Filter/Export tabbed panel provides different options to export the filtered results. For instance, users can obtain a summary of the species found in each basin. A richness map wherein each basin is coded by color according to its total species richness is obtained by click on Close button


Click on Export maps to obtain: To grouped summary: summary of the species found in each basin

To presence data: species locations and associated environmental data

Click Close to see the richness map

Click on Export Metric to compute metrics, including richness,

rarity, AOO index, EOO index, path index or

latitudinal range index


Richness map and its corresponding scale are shown in MRFinder after the user click on Close button of Filter/Export panel.


Click on this icon to save the richness map as an

image

Click on this button to show again the Filter/Export panel


MRFinder also provides a method to estimate the area of shapes (river basins in this example). A report is generated in CSV format with both the total area and the area for each type of habitat within each shape.


Go to menu Export/Shape areas summary report


A shape can also be used as a pattern to clip a raster. The clipping facility is useful for obtaining rasters of environmental variables for a specific area. A repot with a summary of areas and statistics for each shape and variable is also generated.


1. Go to menu Export/Environmental data for shapes

2. Select the environmental variables (Note: environmental data be

previously integrated into ModestR)

3. Click on Accept


Shapes can also be used in MapEditor and MRMapping. They are added to the map in the menu Layers>Shapes>Add shapes. In addition to visualization purposes, these applications also include similar facilities to compute areas or clip rasters.


Go to menu Shapes/Add shapes


ModesR also provides tools to evaluate the environmental quality of shapes (river basins in this example). The first step is to run MapMaker and create an environmental layer*


1. Go to menu Mapping/Niche of occurrence/Create new environmental layer

2. Select the variables to be included in the environmental layer

3. Click on Continue and follow the instructions using default options *

* Tutorial “Creating environmental layers” explains step by step how to

create an environmental layer. Details on different options are also

available in the ModestR manual.




Once the environmental layer is created, add the shapes (river basins) to the map. Go to menu Layers>Shapes>Add shapes and follow the previous instructions (slides 5-8)


1

2

3


Shapes added to the map will be shown semitransparent by default.


You can place the mouse over any shape

to see its name


Now we can calculate the environmental conditions of the areas corresponding to the shapes, according to the environmental layer previously built.


Go to menu Mapping/Niche of occurrence/Polar data maps for shapes


Next, a dialog with the whole data map of the current environmental layer will be shown. In this dialog you can select one of the shapes previously added to the map.


By default, the data map of the whole environmental

layer is shown

Select one of the shapes previously added to the map to see its specific data map

Clicking on the Exportbutton, a report including

this type of graph, as well as other data, is exported for each shape of the left list


MapMaker will show the parts of the whole environmental layer corresponding to the environmental conditions present in the selected shape, providing an insight of the diversity of the environmental conditions in this area and its relationship with the whole environmental conditions.


Select one of the shapes previously added to the map to see its specific

data map

Only the conditions present in the selected shape are shown in the

displayed data map. This can provide an overview of

the kind of environmental conditions present in this area, regarding its place within the

polar coordinates system.The gray background represents the whole environmental layer,

allowing users to see the selected area within the whole map.


In addition to data corresponding to a specific region, the density of its environmental conditions can also be displayed, providing an overview of which conditions are more frequent in the selected shape. It is useful for comparing regions.


In the right tabbed panel, select the Region density

map.

The conditions present in the selected shape

are shown as a density graph. Areas with a

warmer color (green, yellow, red) indicate

more frequent conditions than areas

with colder colors (blue).



Data can be projected to the corresponding geographic area to be displayed in the world map by clicking on the Show button

Clicking on the Show button, the corresponding data for the selected shape (either from the density

map or from the data map) will be shown in the world map as raster data.


It was theStep by step tutorial:

Working with shapes in ModestR

Thank you for your interest.

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You can find this one and other tutorials in http://www.ipez.es/ModestR

